Multiple sequence alignment - TraesCS3D01G301600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G301600 chr3D 100.000 3958 0 0 1 3958 415980068 415976111 0.000000e+00 7310
1 TraesCS3D01G301600 chr7D 88.035 1613 116 49 1599 3164 6389421 6387839 0.000000e+00 1838
2 TraesCS3D01G301600 chr7D 88.377 1497 54 32 1 1466 6390945 6389538 0.000000e+00 1690
3 TraesCS3D01G301600 chr7D 89.027 802 73 15 3160 3957 30263761 30262971 0.000000e+00 979
4 TraesCS3D01G301600 chr7D 84.298 121 14 3 1482 1598 530085673 530085554 3.230000e-21 113
5 TraesCS3D01G301600 chr3A 86.492 1525 86 36 1 1460 534363729 534365198 0.000000e+00 1565
6 TraesCS3D01G301600 chr3A 89.437 994 63 22 2193 3164 534366482 534367455 0.000000e+00 1216
7 TraesCS3D01G301600 chr3A 88.889 522 36 16 1604 2118 534365381 534365887 1.210000e-174 623
8 TraesCS3D01G301600 chr3A 93.976 83 2 3 2123 2203 534366383 534366464 5.370000e-24 122
9 TraesCS3D01G301600 chr3B 87.245 1176 80 39 1 1122 542552792 542551633 0.000000e+00 1277
10 TraesCS3D01G301600 chr3B 86.780 885 62 31 2291 3164 542550483 542549643 0.000000e+00 935
11 TraesCS3D01G301600 chr3B 88.761 436 29 13 1599 2033 542551156 542550740 2.110000e-142 516
12 TraesCS3D01G301600 chr3B 83.673 392 36 13 1167 1552 542551539 542551170 1.050000e-90 344
13 TraesCS3D01G301600 chr3B 89.908 109 5 3 2021 2127 542550724 542550620 6.900000e-28 135
14 TraesCS3D01G301600 chr3B 96.774 62 2 0 2129 2190 542550552 542550491 1.950000e-18 104
15 TraesCS3D01G301600 chr2D 92.174 805 52 10 3157 3958 174425981 174425185 0.000000e+00 1127
16 TraesCS3D01G301600 chr2D 88.875 800 72 17 3164 3958 614392903 614392116 0.000000e+00 968
17 TraesCS3D01G301600 chr2D 90.179 112 10 1 1481 1592 633850175 633850285 1.150000e-30 145
18 TraesCS3D01G301600 chr2D 83.206 131 11 10 1483 1606 380408402 380408276 4.180000e-20 110
19 TraesCS3D01G301600 chr7B 91.656 803 54 9 3164 3958 679450844 679451641 0.000000e+00 1099
20 TraesCS3D01G301600 chr5B 91.521 802 59 9 3161 3958 416547689 416548485 0.000000e+00 1096
21 TraesCS3D01G301600 chr5B 87.705 122 11 2 1483 1604 477078441 477078558 5.330000e-29 139
22 TraesCS3D01G301600 chr5A 91.397 802 57 12 3161 3958 706070619 706071412 0.000000e+00 1088
23 TraesCS3D01G301600 chr1D 88.889 801 72 17 3163 3958 1835682 1834894 0.000000e+00 970
24 TraesCS3D01G301600 chr1D 88.778 802 71 18 3163 3958 408882608 408881820 0.000000e+00 965
25 TraesCS3D01G301600 chr1B 84.491 806 100 22 3160 3958 40422362 40423149 0.000000e+00 773
26 TraesCS3D01G301600 chr4B 88.333 120 8 3 1481 1595 545016605 545016487 5.330000e-29 139
27 TraesCS3D01G301600 chr4B 86.087 115 11 2 1481 1595 640009161 640009052 6.950000e-23 119
28 TraesCS3D01G301600 chr1A 88.034 117 11 3 1482 1595 399505739 399505855 6.900000e-28 135
29 TraesCS3D01G301600 chr6D 85.965 114 16 0 1482 1595 91146397 91146284 5.370000e-24 122
30 TraesCS3D01G301600 chr7A 84.553 123 13 4 1478 1595 609653165 609653044 2.500000e-22 117


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G301600 chr3D 415976111 415980068 3957 True 7310.000000 7310 100.000000 1 3958 1 chr3D.!!$R1 3957
1 TraesCS3D01G301600 chr7D 6387839 6390945 3106 True 1764.000000 1838 88.206000 1 3164 2 chr7D.!!$R3 3163
2 TraesCS3D01G301600 chr7D 30262971 30263761 790 True 979.000000 979 89.027000 3160 3957 1 chr7D.!!$R1 797
3 TraesCS3D01G301600 chr3A 534363729 534367455 3726 False 881.500000 1565 89.698500 1 3164 4 chr3A.!!$F1 3163
4 TraesCS3D01G301600 chr3B 542549643 542552792 3149 True 551.833333 1277 88.856833 1 3164 6 chr3B.!!$R1 3163
5 TraesCS3D01G301600 chr2D 174425185 174425981 796 True 1127.000000 1127 92.174000 3157 3958 1 chr2D.!!$R1 801
6 TraesCS3D01G301600 chr2D 614392116 614392903 787 True 968.000000 968 88.875000 3164 3958 1 chr2D.!!$R3 794
7 TraesCS3D01G301600 chr7B 679450844 679451641 797 False 1099.000000 1099 91.656000 3164 3958 1 chr7B.!!$F1 794
8 TraesCS3D01G301600 chr5B 416547689 416548485 796 False 1096.000000 1096 91.521000 3161 3958 1 chr5B.!!$F1 797
9 TraesCS3D01G301600 chr5A 706070619 706071412 793 False 1088.000000 1088 91.397000 3161 3958 1 chr5A.!!$F1 797
10 TraesCS3D01G301600 chr1D 1834894 1835682 788 True 970.000000 970 88.889000 3163 3958 1 chr1D.!!$R1 795
11 TraesCS3D01G301600 chr1D 408881820 408882608 788 True 965.000000 965 88.778000 3163 3958 1 chr1D.!!$R2 795
12 TraesCS3D01G301600 chr1B 40422362 40423149 787 False 773.000000 773 84.491000 3160 3958 1 chr1B.!!$F1 798

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
118 123 0.250295 TTGGTTTGGTCGCTCCTCTG 60.250 55.0 0.0 0.0 37.07 3.35 F
1183 1392 0.396974 TGTTCCAAACCAGGCAGCTT 60.397 50.0 0.0 0.0 0.00 3.74 F
2376 3303 0.245813 GGGTCGGTCTCTGTTACCAC 59.754 60.0 0.0 0.0 36.78 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 2073 2.634940 TGCCTTTCAGCTCTACAAGACT 59.365 45.455 0.00 0.0 0.00 3.24 R
2556 3483 0.108424 GAGGATGCACTGAAGCGAGT 60.108 55.000 0.00 0.0 37.31 4.18 R
3441 4408 0.468226 AGAACAGCGTTGTCCAAGGA 59.532 50.000 5.04 0.0 36.23 3.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 123 0.250295 TTGGTTTGGTCGCTCCTCTG 60.250 55.000 0.00 0.00 37.07 3.35
128 133 2.262915 CTCCTCTGTTCGCCGCTT 59.737 61.111 0.00 0.00 0.00 4.68
189 221 1.657094 CTTTGGTACGTGTACATCCGC 59.343 52.381 11.89 0.00 37.78 5.54
422 551 6.092396 GGAGCTGATCTATGTGCATAATTCTG 59.908 42.308 0.00 0.00 0.00 3.02
428 557 1.832883 TGTGCATAATTCTGGCGGTT 58.167 45.000 0.00 0.00 0.00 4.44
456 585 3.124560 TGCGATGAAGTTGACGTGTTTA 58.875 40.909 0.00 0.00 0.00 2.01
553 686 1.714414 CAGACTCGTACTCCCGTCG 59.286 63.158 0.00 0.00 0.00 5.12
734 868 2.423031 CGCCACGTGTCTTCGTACG 61.423 63.158 15.65 9.53 42.27 3.67
756 890 0.788391 CACTCCGTTTAAGCCACGTC 59.212 55.000 0.00 0.00 35.81 4.34
1122 1282 8.248945 GCAAGGGTACGTATATTCTGTGTATAT 58.751 37.037 0.00 0.00 0.00 0.86
1183 1392 0.396974 TGTTCCAAACCAGGCAGCTT 60.397 50.000 0.00 0.00 0.00 3.74
1187 1396 2.672098 TCCAAACCAGGCAGCTTTTTA 58.328 42.857 0.00 0.00 0.00 1.52
1200 1410 4.026052 CAGCTTTTTATCCCTCCCATGTT 58.974 43.478 0.00 0.00 0.00 2.71
1304 1514 1.283029 TCCCTCCATTCTTCCTTGCTG 59.717 52.381 0.00 0.00 0.00 4.41
1311 1524 6.774656 CCTCCATTCTTCCTTGCTGTAATAAT 59.225 38.462 0.00 0.00 0.00 1.28
1453 1672 6.036517 CAGATAGTTGTAGAACAGGATTGCAC 59.963 42.308 5.45 0.00 34.17 4.57
1454 1673 4.357918 AGTTGTAGAACAGGATTGCACT 57.642 40.909 5.45 0.00 34.17 4.40
1455 1674 5.483685 AGTTGTAGAACAGGATTGCACTA 57.516 39.130 5.45 0.00 34.17 2.74
1456 1675 6.054860 AGTTGTAGAACAGGATTGCACTAT 57.945 37.500 5.45 0.00 34.17 2.12
1457 1676 7.182817 AGTTGTAGAACAGGATTGCACTATA 57.817 36.000 5.45 0.00 34.17 1.31
1458 1677 7.620880 AGTTGTAGAACAGGATTGCACTATAA 58.379 34.615 5.45 0.00 34.17 0.98
1459 1678 7.766278 AGTTGTAGAACAGGATTGCACTATAAG 59.234 37.037 5.45 0.00 34.17 1.73
1460 1679 7.182817 TGTAGAACAGGATTGCACTATAAGT 57.817 36.000 0.00 0.00 0.00 2.24
1494 1719 6.602406 GTCTACAGATTTGTACTCCCTCTGTA 59.398 42.308 18.42 18.42 43.42 2.74
1495 1720 7.122353 GTCTACAGATTTGTACTCCCTCTGTAA 59.878 40.741 19.25 12.53 44.44 2.41
1496 1721 6.681729 ACAGATTTGTACTCCCTCTGTAAA 57.318 37.500 14.86 0.00 43.42 2.01
1497 1722 6.702329 ACAGATTTGTACTCCCTCTGTAAAG 58.298 40.000 14.86 0.00 43.42 1.85
1593 1867 7.498239 GCTTTTATATTTCTTTACGGAGGGAGT 59.502 37.037 0.00 0.00 0.00 3.85
1639 1914 2.661718 TCTTTGACAAACCCCCTCAAC 58.338 47.619 0.00 0.00 0.00 3.18
1792 2073 6.258354 TGGTAGGTTTCTCATGGTTCTAGTA 58.742 40.000 0.00 0.00 0.00 1.82
1793 2074 6.380274 TGGTAGGTTTCTCATGGTTCTAGTAG 59.620 42.308 0.00 0.00 0.00 2.57
1794 2075 6.380560 GGTAGGTTTCTCATGGTTCTAGTAGT 59.619 42.308 0.00 0.00 0.00 2.73
1798 2079 6.814146 GGTTTCTCATGGTTCTAGTAGTCTTG 59.186 42.308 0.00 0.00 0.00 3.02
1847 2128 1.135689 GGCCATCTTTTGCACGTGTAG 60.136 52.381 18.38 9.73 0.00 2.74
1863 2144 3.119919 CGTGTAGCTCTACCGTTTCTCTT 60.120 47.826 0.00 0.00 35.26 2.85
1889 2170 4.160626 GTGATTAGTGACCTACCTCAGCTT 59.839 45.833 0.00 0.00 0.00 3.74
1943 2224 1.530013 CTCTACAACACCCCGGACGT 61.530 60.000 0.73 0.00 0.00 4.34
2019 2345 8.142551 AGAGGATTCTTGATAAACGTATGTACC 58.857 37.037 0.00 0.00 0.00 3.34
2075 2401 5.578157 AAGAACCCTCCTGCTAAGTTAAA 57.422 39.130 0.00 0.00 0.00 1.52
2259 3177 4.027458 CGAACAATGCACAAAGAAACACAG 60.027 41.667 0.00 0.00 0.00 3.66
2287 3205 8.806146 ACAAATAGTACTGCAATGAAAAGGAAT 58.194 29.630 5.39 0.00 0.00 3.01
2297 3223 5.062558 GCAATGAAAAGGAATTGATGAACGG 59.937 40.000 0.00 0.00 36.13 4.44
2316 3242 2.729882 CGGAGGTGCTTATATACGCAAC 59.270 50.000 18.89 18.89 43.96 4.17
2334 3260 3.103738 CAACTGCGATTGCTATTGCTTC 58.896 45.455 19.16 0.00 41.09 3.86
2341 3267 6.800632 GCGATTGCTATTGCTTCCTGCATT 62.801 45.833 12.51 0.00 44.61 3.56
2372 3299 1.616865 CACTTGGGTCGGTCTCTGTTA 59.383 52.381 0.00 0.00 0.00 2.41
2376 3303 0.245813 GGGTCGGTCTCTGTTACCAC 59.754 60.000 0.00 0.00 36.78 4.16
2399 3326 1.818221 GCTTGTGTGTCGACGTGTCC 61.818 60.000 11.62 0.00 0.00 4.02
2402 3329 1.065273 GTGTGTCGACGTGTCCTGT 59.935 57.895 11.62 0.00 0.00 4.00
2438 3365 0.874607 AACAGTCGTGACAAGGACGC 60.875 55.000 2.44 0.00 44.23 5.19
2457 3384 2.620242 GCTGCCCACCACAATTTAATG 58.380 47.619 0.00 0.00 0.00 1.90
2476 3403 0.305313 GTTGCTCGTTTACGTTGCCA 59.695 50.000 15.60 6.63 40.80 4.92
2477 3404 1.069500 GTTGCTCGTTTACGTTGCCAT 60.069 47.619 15.60 0.00 40.80 4.40
2479 3406 1.604755 TGCTCGTTTACGTTGCCATTT 59.395 42.857 15.60 0.00 40.80 2.32
2480 3407 2.806818 TGCTCGTTTACGTTGCCATTTA 59.193 40.909 15.60 0.84 40.80 1.40
2481 3408 3.158268 GCTCGTTTACGTTGCCATTTAC 58.842 45.455 0.00 0.00 40.80 2.01
2482 3409 3.364167 GCTCGTTTACGTTGCCATTTACA 60.364 43.478 0.00 0.00 40.80 2.41
2483 3410 4.670735 GCTCGTTTACGTTGCCATTTACAT 60.671 41.667 0.00 0.00 40.80 2.29
2484 3411 5.446206 GCTCGTTTACGTTGCCATTTACATA 60.446 40.000 0.00 0.00 40.80 2.29
2485 3412 6.665474 TCGTTTACGTTGCCATTTACATAT 57.335 33.333 0.00 0.00 40.80 1.78
2486 3413 6.479436 TCGTTTACGTTGCCATTTACATATG 58.521 36.000 0.00 0.00 40.80 1.78
2487 3414 6.092396 TCGTTTACGTTGCCATTTACATATGT 59.908 34.615 13.93 13.93 40.80 2.29
2488 3415 7.277319 TCGTTTACGTTGCCATTTACATATGTA 59.723 33.333 11.62 11.62 40.80 2.29
2489 3416 7.903946 CGTTTACGTTGCCATTTACATATGTAA 59.096 33.333 21.73 21.73 35.33 2.41
2490 3417 9.724839 GTTTACGTTGCCATTTACATATGTAAT 57.275 29.630 25.09 14.34 39.89 1.89
2556 3483 1.514657 GCACGTACGTACATCGGCA 60.515 57.895 22.34 0.00 44.69 5.69
2558 3485 0.179181 CACGTACGTACATCGGCACT 60.179 55.000 22.34 0.00 44.69 4.40
2560 3487 0.922560 CGTACGTACATCGGCACTCG 60.923 60.000 24.50 3.65 44.69 4.18
2565 3492 0.457853 GTACATCGGCACTCGCTTCA 60.458 55.000 0.00 0.00 39.05 3.02
2568 3495 1.446792 ATCGGCACTCGCTTCAGTG 60.447 57.895 3.57 3.57 45.82 3.66
2573 3500 2.084844 CACTCGCTTCAGTGCATCC 58.915 57.895 0.00 0.00 37.58 3.51
2574 3501 0.390866 CACTCGCTTCAGTGCATCCT 60.391 55.000 0.00 0.00 37.58 3.24
2575 3502 0.108424 ACTCGCTTCAGTGCATCCTC 60.108 55.000 0.00 0.00 0.00 3.71
2576 3503 0.175302 CTCGCTTCAGTGCATCCTCT 59.825 55.000 0.00 0.00 0.00 3.69
2577 3504 1.406898 CTCGCTTCAGTGCATCCTCTA 59.593 52.381 0.00 0.00 0.00 2.43
2589 3516 5.784390 AGTGCATCCTCTATGGTCTATGAAT 59.216 40.000 0.00 0.00 35.99 2.57
2592 3519 8.263640 GTGCATCCTCTATGGTCTATGAATATT 58.736 37.037 0.00 0.00 35.99 1.28
2593 3520 9.492730 TGCATCCTCTATGGTCTATGAATATTA 57.507 33.333 0.00 0.00 35.99 0.98
2641 3582 5.596772 TCTTTACACCCGTCATGAGATGATA 59.403 40.000 0.00 0.00 42.04 2.15
2643 3584 4.327982 ACACCCGTCATGAGATGATAAG 57.672 45.455 0.00 0.00 42.04 1.73
2650 3591 6.405286 CCCGTCATGAGATGATAAGTAGATCC 60.405 46.154 0.00 0.00 42.04 3.36
2654 3595 9.202273 GTCATGAGATGATAAGTAGATCCAAAC 57.798 37.037 0.00 0.00 42.04 2.93
2873 3817 3.878519 CTCGGCTCGTCGGAGGAC 61.879 72.222 0.00 0.00 40.80 3.85
3174 4134 7.222999 AGACTACTTCAGTTCTGAAGAAAAACG 59.777 37.037 34.51 21.57 45.93 3.60
3235 4195 8.537728 TTGATTCATCCAGGCTTTTATATGTT 57.462 30.769 0.00 0.00 0.00 2.71
3238 4198 9.507329 GATTCATCCAGGCTTTTATATGTTCTA 57.493 33.333 0.00 0.00 0.00 2.10
3295 4256 3.365820 CGCATCGTTTAGAAAAGGTACGT 59.634 43.478 0.00 0.00 34.15 3.57
3325 4286 2.289547 CGGAAAGACATGACAACGGTTT 59.710 45.455 0.00 0.00 0.00 3.27
3329 4290 5.008316 GGAAAGACATGACAACGGTTTACTT 59.992 40.000 0.00 0.00 0.00 2.24
3342 4309 6.194796 ACGGTTTACTTTATACTGCGTCTA 57.805 37.500 0.00 0.00 0.00 2.59
3349 4316 6.263516 ACTTTATACTGCGTCTAGACAACA 57.736 37.500 22.37 17.45 0.00 3.33
3367 4334 2.344592 ACACCAGGATTCTAACCACCA 58.655 47.619 0.00 0.00 0.00 4.17
3384 4351 7.989947 AACCACCAGTTAGAATATCCTAAGA 57.010 36.000 0.00 0.00 36.74 2.10
3459 4426 0.868406 CTCCTTGGACAACGCTGTTC 59.132 55.000 0.00 0.00 35.30 3.18
3463 4430 2.480419 CCTTGGACAACGCTGTTCTTAG 59.520 50.000 0.00 0.00 35.30 2.18
3588 4556 6.335781 ACTATTTATGCCCCTGTAGGAAAA 57.664 37.500 0.00 0.00 38.24 2.29
3594 4562 9.890915 ATTTATGCCCCTGTAGGAAAATATAAA 57.109 29.630 0.00 4.52 38.24 1.40
3679 4647 5.710099 AGAAATCCGTTGGAAAGCTCATAAA 59.290 36.000 0.00 0.00 34.34 1.40
3717 4685 4.023137 CCCCCTGAACATGGCAAG 57.977 61.111 0.00 0.00 0.00 4.01
3718 4686 1.383799 CCCCCTGAACATGGCAAGA 59.616 57.895 0.00 0.00 0.00 3.02
3721 4689 2.181975 CCCCTGAACATGGCAAGATTT 58.818 47.619 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 89 1.160137 CAAACCAAGAGAAGGGAGCG 58.840 55.000 0.00 0.00 0.00 5.03
118 123 1.668151 ACCAGAGAAAGCGGCGAAC 60.668 57.895 12.98 0.00 0.00 3.95
128 133 1.003580 GAAGCCCATGACACCAGAGAA 59.996 52.381 0.00 0.00 0.00 2.87
189 221 2.094258 ACGTGCATGCTTACTTTCATCG 59.906 45.455 20.33 9.74 0.00 3.84
293 376 2.135933 GTACGTGCTCAGTGCTTTTCT 58.864 47.619 0.00 0.00 43.37 2.52
294 377 1.136611 CGTACGTGCTCAGTGCTTTTC 60.137 52.381 7.22 0.00 43.37 2.29
295 378 0.859232 CGTACGTGCTCAGTGCTTTT 59.141 50.000 7.22 0.00 43.37 2.27
296 379 0.249322 ACGTACGTGCTCAGTGCTTT 60.249 50.000 22.14 0.00 43.37 3.51
335 446 1.510623 CGACTCGTACGTGGAACCG 60.511 63.158 20.21 13.53 0.00 4.44
337 448 0.040067 AACCGACTCGTACGTGGAAC 60.040 55.000 20.21 10.66 0.00 3.62
341 452 0.160182 GCAAAACCGACTCGTACGTG 59.840 55.000 16.05 15.64 0.00 4.49
422 551 2.414785 ATCGCATTTCCCAACCGCC 61.415 57.895 0.00 0.00 0.00 6.13
428 557 2.487762 GTCAACTTCATCGCATTTCCCA 59.512 45.455 0.00 0.00 0.00 4.37
456 585 1.518056 CTGCACGTGGCTCCACAAAT 61.518 55.000 18.88 1.30 46.47 2.32
553 686 2.802247 TCGCCGATCAATCATGATTCAC 59.198 45.455 18.16 11.00 46.30 3.18
621 755 2.045045 CGGCCAATGGGAGCTTGA 60.045 61.111 2.24 0.00 35.59 3.02
734 868 1.302993 TGGCTTAAACGGAGTGGCC 60.303 57.895 0.00 0.00 45.00 5.36
756 890 0.948623 TGTCGTGAATTGACGGGCAG 60.949 55.000 17.35 0.00 39.88 4.85
835 969 2.417719 AGAATTTGCTGTGGACGAGAC 58.582 47.619 0.00 0.00 0.00 3.36
1046 1206 3.785859 GCTCCGCCTCCATGGACA 61.786 66.667 11.44 0.00 38.35 4.02
1183 1392 6.156083 GGATTTCAAACATGGGAGGGATAAAA 59.844 38.462 0.00 0.00 0.00 1.52
1187 1396 3.646534 GGATTTCAAACATGGGAGGGAT 58.353 45.455 0.00 0.00 0.00 3.85
1200 1410 3.054434 AGTGGTGATGGATCGGATTTCAA 60.054 43.478 0.00 0.00 0.00 2.69
1566 1840 6.480981 TCCCTCCGTAAAGAAATATAAAAGCG 59.519 38.462 0.00 0.00 0.00 4.68
1639 1914 4.884668 TTTAGTAGGAACACTGTCCCAG 57.115 45.455 0.00 0.00 38.59 4.45
1673 1953 8.774546 ACTTCTTCCTCTATCATCATTGTCTA 57.225 34.615 0.00 0.00 0.00 2.59
1677 1957 8.728337 TTCAACTTCTTCCTCTATCATCATTG 57.272 34.615 0.00 0.00 0.00 2.82
1680 1960 8.378565 AGTTTTCAACTTCTTCCTCTATCATCA 58.621 33.333 0.00 0.00 39.04 3.07
1681 1961 8.785329 AGTTTTCAACTTCTTCCTCTATCATC 57.215 34.615 0.00 0.00 39.04 2.92
1686 1966 9.901172 AACTTTAGTTTTCAACTTCTTCCTCTA 57.099 29.630 0.00 0.00 42.81 2.43
1687 1967 8.809468 AACTTTAGTTTTCAACTTCTTCCTCT 57.191 30.769 0.00 0.00 42.81 3.69
1792 2073 2.634940 TGCCTTTCAGCTCTACAAGACT 59.365 45.455 0.00 0.00 0.00 3.24
1793 2074 3.045601 TGCCTTTCAGCTCTACAAGAC 57.954 47.619 0.00 0.00 0.00 3.01
1794 2075 3.769739 TTGCCTTTCAGCTCTACAAGA 57.230 42.857 0.00 0.00 0.00 3.02
1798 2079 7.088589 TGAATAATTTGCCTTTCAGCTCTAC 57.911 36.000 0.00 0.00 0.00 2.59
1847 2128 2.737252 CACCAAAGAGAAACGGTAGAGC 59.263 50.000 0.00 0.00 0.00 4.09
1863 2144 4.422057 TGAGGTAGGTCACTAATCACCAA 58.578 43.478 0.00 0.00 34.80 3.67
1889 2170 3.181479 CGGATGGAATCGACTTTACAGGA 60.181 47.826 0.00 0.00 46.86 3.86
1943 2224 4.214332 TGTGTGCATGCATACGAAACTTAA 59.786 37.500 33.32 16.82 40.26 1.85
2127 3011 9.753674 TTTATCTATTCACTTCAACCAGGAAAT 57.246 29.630 0.00 0.00 0.00 2.17
2194 3110 9.646336 CCAAGTTTACAAAGTCGTATATATTGC 57.354 33.333 0.00 0.00 0.00 3.56
2237 3154 5.101628 TCTGTGTTTCTTTGTGCATTGTTC 58.898 37.500 0.00 0.00 0.00 3.18
2259 3177 8.296713 TCCTTTTCATTGCAGTACTATTTGTTC 58.703 33.333 0.00 0.00 0.00 3.18
2287 3205 3.627395 ATAAGCACCTCCGTTCATCAA 57.373 42.857 0.00 0.00 0.00 2.57
2297 3223 3.184581 GCAGTTGCGTATATAAGCACCTC 59.815 47.826 20.88 14.40 43.69 3.85
2316 3242 1.945394 AGGAAGCAATAGCAATCGCAG 59.055 47.619 0.00 0.00 45.49 5.18
2334 3260 0.245266 TGCATGAACAGCAATGCAGG 59.755 50.000 8.35 1.12 44.01 4.85
2341 3267 0.467844 ACCCAAGTGCATGAACAGCA 60.468 50.000 6.60 0.00 40.19 4.41
2372 3299 1.151777 CGACACACAAGCTTCGTGGT 61.152 55.000 23.00 18.95 38.74 4.16
2376 3303 1.206745 ACGTCGACACACAAGCTTCG 61.207 55.000 17.16 0.00 0.00 3.79
2402 3329 1.478916 TGTTCTCTGTTGTGACGGACA 59.521 47.619 0.00 0.00 36.26 4.02
2438 3365 3.959535 ACATTAAATTGTGGTGGGCAG 57.040 42.857 0.00 0.00 0.00 4.85
2457 3384 0.305313 TGGCAACGTAAACGAGCAAC 59.695 50.000 19.86 9.17 42.28 4.17
2481 3408 9.077674 GCGAGTACAGAAGGAATATTACATATG 57.922 37.037 0.00 0.00 0.00 1.78
2482 3409 8.803235 TGCGAGTACAGAAGGAATATTACATAT 58.197 33.333 0.00 0.00 0.00 1.78
2483 3410 8.173542 TGCGAGTACAGAAGGAATATTACATA 57.826 34.615 0.00 0.00 0.00 2.29
2484 3411 7.050970 TGCGAGTACAGAAGGAATATTACAT 57.949 36.000 0.00 0.00 0.00 2.29
2485 3412 6.459670 TGCGAGTACAGAAGGAATATTACA 57.540 37.500 0.00 0.00 0.00 2.41
2486 3413 7.270793 CGTATGCGAGTACAGAAGGAATATTAC 59.729 40.741 0.00 0.00 41.33 1.89
2487 3414 7.303261 CGTATGCGAGTACAGAAGGAATATTA 58.697 38.462 0.00 0.00 41.33 0.98
2488 3415 6.150318 CGTATGCGAGTACAGAAGGAATATT 58.850 40.000 0.00 0.00 41.33 1.28
2489 3416 5.700846 CGTATGCGAGTACAGAAGGAATAT 58.299 41.667 0.00 0.00 41.33 1.28
2490 3417 4.556104 GCGTATGCGAGTACAGAAGGAATA 60.556 45.833 7.60 0.00 41.33 1.75
2556 3483 0.108424 GAGGATGCACTGAAGCGAGT 60.108 55.000 0.00 0.00 37.31 4.18
2558 3485 1.474330 TAGAGGATGCACTGAAGCGA 58.526 50.000 0.00 0.00 37.31 4.93
2560 3487 2.158842 ACCATAGAGGATGCACTGAAGC 60.159 50.000 0.00 0.00 41.22 3.86
2565 3492 4.745351 TCATAGACCATAGAGGATGCACT 58.255 43.478 0.00 0.00 41.22 4.40
2623 3554 4.327982 ACTTATCATCTCATGACGGGTG 57.672 45.455 0.00 0.00 43.01 4.61
2627 3558 7.150783 TGGATCTACTTATCATCTCATGACG 57.849 40.000 0.00 0.00 43.01 4.35
2711 3652 2.973082 GCCGCCTCCTGCAATTTT 59.027 55.556 0.00 0.00 41.33 1.82
3004 3961 5.527582 CCGATGCTAAAGCTAAAATACTGGT 59.472 40.000 3.26 0.00 42.66 4.00
3044 4002 1.586028 CAGGACGCACCCCAAAATG 59.414 57.895 0.00 0.00 40.05 2.32
3174 4134 6.652481 TCACTCCATTCACTTCAATCTTTCTC 59.348 38.462 0.00 0.00 0.00 2.87
3235 4195 4.919168 CGACACTGTAAACATCCGTTTAGA 59.081 41.667 0.00 0.00 45.83 2.10
3238 4198 3.719924 TCGACACTGTAAACATCCGTTT 58.280 40.909 0.00 0.00 46.94 3.60
3342 4309 3.650942 TGGTTAGAATCCTGGTGTTGTCT 59.349 43.478 0.00 0.00 0.00 3.41
3349 4316 2.632537 ACTGGTGGTTAGAATCCTGGT 58.367 47.619 0.00 0.00 0.00 4.00
3441 4408 0.468226 AGAACAGCGTTGTCCAAGGA 59.532 50.000 5.04 0.00 36.23 3.36
3463 4430 8.715191 ATGTAGATTCTCAAGACAATGAAGAC 57.285 34.615 0.00 0.00 0.00 3.01
3496 4463 8.562892 CAAGAAGACACAAGACTTTTGATACAT 58.437 33.333 8.32 0.00 30.00 2.29
3497 4464 7.768582 TCAAGAAGACACAAGACTTTTGATACA 59.231 33.333 8.32 0.00 30.54 2.29
3552 4519 8.793592 GGGGCATAAATAGTACAAGATTAAAGG 58.206 37.037 0.00 0.00 0.00 3.11
3575 4542 8.059461 AGTTCCTTTTATATTTTCCTACAGGGG 58.941 37.037 0.00 0.00 35.41 4.79
3712 4680 3.585862 TGAGACGACTACAAATCTTGCC 58.414 45.455 0.00 0.00 0.00 4.52
3717 4685 7.381678 GGTATTGGTATGAGACGACTACAAATC 59.618 40.741 0.00 0.00 0.00 2.17
3718 4686 7.147794 TGGTATTGGTATGAGACGACTACAAAT 60.148 37.037 0.00 0.00 0.00 2.32
3721 4689 5.195185 TGGTATTGGTATGAGACGACTACA 58.805 41.667 0.00 0.00 0.00 2.74
3765 4733 3.192844 TCACTAAGTCTTTACCAGGAGCG 59.807 47.826 0.00 0.00 0.00 5.03


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.